python3 + rpy + pyodb + vertica 7 = Linux segfault

Hi Folks,

I've discovered a python-vertica stack configuration that causes a segmentation 
fault on our Linux cluster. I'd really appreciate your help in deciding how to 
proceed with a solution. I've attached as much information as I can to help 
figure this out.

The summary: When running in a virtualenv, if I import rpy2.objects then pyodb 
and then try to execute certain queries, I get the segfault. Interestingly, if 
I swap the import order, it seems to work OK (!) Testing on previous versions 
of pyodb have the segfault happening at connect() instead of execute().

Thanks very much,

matt

** commands to install the stack via virtualenv

/share/apps/python3/bin/python3.3 ~/bin/virtualenv.py --no-site-packages 
~/virtualenvs/vertica-test
source ~/virtualenvs/vertica-test/bin/activate

pip install http://pyodbc.googlecode.com/files/pyodbc-3.0.7.zip
-> Successfully installed pyodbc

pip install rpy2
-> Successfully installed rpy2

** commands in interpreter to reproduce the segfault

# NB: bad username or password -> segfault at connect()
# NB: if the import order is switched -> NO segfault

[cornell@wright ~]$ source ~/virtualenvs/vertica-test/bin/activate

(vertica-test)[cornell@wright ~]$ python3.3
Python 3.3.2 (default, May 16 2013, 11:31:48) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy2.robjects
>>> import pyodbc
>>> conn = pyodbc.connect('DSN=vertica_kdl_dsn;UID=xx;PWD=xx')
>>> curs = conn.cursor()
>>> curs.execute('DROP TABLE IF EXISTS foo')
Segmentation fault

(vertica-test)[cornell@wright ~]$ python3.3
Python 3.3.2 (default, May 16 2013, 11:31:48) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyodbc
>>> import rpy2.robjects
>>> conn = pyodbc.connect('DSN=vertica_kdl_dsn;UID=xx;PWD=xx')
>>> curs = conn.cursor()
>>> curs.execute('DROP TABLE IF EXISTS foo')
<pyodbc.Cursor object at 0x7f8508b5fe10>
>>> 

** versions

Python 3.3.2 (default, May 16 2013, 11:31:48) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux

>>> rpy2.__version__
'2.3.8'

>>> pyodbc.version
'3.0.7'
>>> pyodbc.SQL_DBMS_VER
18
>>> pyodbc.SQL_DM_VER
171
>>> pyodbc.SQL_DRIVER_ODBC_VER
77
>>> pyodbc.SQL_DRIVER_VER
7
>>> pyodbc.SQL_ODBC_VER
10

$ isql --version
unixODBC 2.2.14

/opt/vertica/lib64:
  lrwxrwxrwx  1 root root       23 Dec 18 09:43 libverticaodbc.so.7.0 -> libverticaodbc.so.7.0.0

[dbadmin@compute-0-0 ~]$ /opt/vertica/bin/adminTools
Vertica Analytic Database 7.0.0-0 Administration Tools

[cornell@wright ~]$ uname -a
Linux wright.cs.umass.edu 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 
UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
[cornell@wright ~]$ cat /proc/version 
Linux version 2.6.32-279.14.1.el6.x86_64 (mockbuild@c6b8.bsys.dev.centos.org) 
(gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Tue Nov 6 23:43:09 
UTC 2012
[cornell@wright ~]$ 

** odbc configuration files

*** /etc/odbcinst.ini

[PostgreSQL]
...

[MySQL]
...

[vertica_driver]
Description     = Vertica 7 ODBC driver
Driver          = /opt/vertica/lib/libverticaodbc.so
Driver64        = /opt/vertica/lib64/libverticaodbc.so
FileUsage       = 1

[ODBC]
Threading       = 1
Trace           = 1
TraceFile       = /tmp/odbctrace.log
Debug           = 1
DebugFile       = /tmp/odbcdebug.log

*** /etc/odbc.ini

[ODBC Data Sources]
vertica_kdl_dsn = kdl database on HP Vertica 7

[vertica_kdl_dsn]
Driver = vertica_driver
Description = ODBC Driver DSN for kdl master database
Servername = compute-0-0
Port = 5433
Database = kdl
Locale = en_US

*** /etc/vertica.ini

[Driver]
DriverManagerEncoding = UTF-16
ODBCInstLib = /usr/lib64/libodbcinst.so
ErrorMessagesPath = /opt/vertica/lib64
LogLevel = 4
LogPath = /tmp

*** odbc trace files: see attached (wright-odbc-trace-2014-01-17)

/tmp/odbctrace.log
/tmp/vertica_odbc_conn_1.log
/tmp/vertica_driver.log

Original issue reported on code.google.com by matthewc...@gmail.com on 17 Jan 2014 at 5:47

Attachments:

Here's some connection information, if that helps:

<code>

>>> import rpy2.robjects
>>> import pyodbc
>>> conn = pyodbc.connect('DSN=vertica_kdl_dsn;UserName=xx;Password=xx')
>>> for attr in vars(pyodbc):
...     try:
...         value = conn.getinfo(getattr(pyodbc, attr))
...         print('{:<40s} | {}'.format(attr, value))
...     except:
...         pass
... 
SQL_SQL_CONFORMANCE                      | 1
SQL_TXN_ISOLATION_OPTION                 | 10
SQL_PROCEDURE_TERM                       | function
SQL_DROP_TRANSLATION                     | 0
SQL_CATALOG_USAGE                        | 0
SQL_SCHEMA_USAGE                         | 21
SQL_NULLABLE                             | 0
SQL_STATIC_CURSOR_ATTRIBUTES2            | 0
SQL_STATIC_CURSOR_ATTRIBUTES1            | 0
SQL_MAX_COLUMNS_IN_TABLE                 | 1600
SQL_GETDATA_EXTENSIONS                   | 15
SQL_INTERVAL_MONTH                       | 0
SQL_LIKE_ESCAPE_CLAUSE                   | True
SQL_TIMEDATE_DIFF_INTERVALS              | 511
SQL_ROW_UPDATES                          | False
SQL_MAX_ROW_SIZE                         | 32000000
SQL_INTERVAL_YEAR                        | 1600
SQL_XOPEN_CLI_YEAR                       | 1995
SQL_INTERVAL_SECOND                      | 0
SQL_INTERVAL_MINUTE                      | 0
SQL_ACTIVE_ENVIRONMENTS                  | 0
SQL_MAX_INDEX_SIZE                       | 0
SQL_TIMEDATE_FUNCTIONS                   | 1998847
SQL_ALTER_TABLE                          | 62312
SQL_CREATE_TABLE                         | 1045
SQL_INTERVAL_DAY_TO_MINUTE               | 511
SQL_SCOPE_SESSION                        | vertica_kdl_dsn
SQL_SQL92_REVOKE                         | 13744
SQL_CREATE_TRANSLATION                   | 0
SQL_MAX_BINARY_LITERAL_LEN               | 0
SQL_PARAM_INPUT                          | 0
SQL_PARAM_ARRAY_ROW_COUNTS               | 1
SQL_COLUMN_ALIAS                         | True
SQL_SQL92_ROW_VALUE_CONSTRUCTOR          | 3
SQL_SCROLL_OPTIONS                       | 1
SQL_SCOPE_TRANSACTION                    | 0
lowercase                                | 0
SQL_BATCH_ROW_COUNT                      | 2
SQL_DYNAMIC_CURSOR_ATTRIBUTES2           | 0
SQL_DYNAMIC_CURSOR_ATTRIBUTES1           | 0
SQL_CATALOG_NAME                         | False
SQL_SUBQUERIES                           | 31
SQL_SCHEMA_TERM                          | schema
SQL_UNION                                | 3
SQL_NEED_LONG_DATA_LEN                   | False
SQL_DATA_SOURCE_READ_ONLY                | False
SQL_DDL_INDEX                            | 0
SQL_NON_NULLABLE_COLUMNS                 | 1
SQL_MAX_IDENTIFIER_LEN                   | 128
SQL_QUOTED_IDENTIFIER_CASE               | 4
SQL_SERVER_NAME                          | compute-0-0
SQL_UNKNOWN_TYPE                         | 0
SQL_NUMERIC                              | vertica_kdl_dsn
SQLWCHAR_SIZE                            | vertica_kdl_dsn
SQL_CORRELATION_NAME                     | 2
SQL_DESCRIBE_PARAMETER                   | False
SQL_INTERVAL_HOUR_TO_MINUTE              | False
SQL_EXPRESSIONS_IN_ORDERBY               | True
SQL_OJ_CAPABILITIES                      | 127
SQL_TABLE_TERM                           | table
SQL_SQL92_FOREIGN_KEY_DELETE_RULE        | 0
SQL_CATALOG_LOCATION                     | 1
SQL_BOOKMARK_PERSISTENCE                 | 0
SQL_MAX_COLUMNS_IN_GROUP_BY              | 0
SQL_CREATE_DOMAIN                        | 0
SQL_INTEGRITY                            | False
SQL_DRIVER_NAME                          | verticaodbcw.so
SQL_TYPE_TIME                            | 0
SQL_DEFAULT_TXN_ISOLATION                | 2
SQL_INFO_SCHEMA_VIEWS                    | 0
SQL_TYPE_TIMESTAMP                       | 4
SQL_SCOPE_CURROW                         | 0
SQL_SQL92_NUMERIC_VALUE_FUNCTIONS        | 46
SQL_ORDER_BY_COLUMNS_IN_SELECT           | True
SQL_TYPE_DATE                            | 21
SQL_CREATE_ASSERTION                     | 0
SQL_INTERVAL_MINUTE_TO_SECOND            | True
SQL_NULLABLE_UNKNOWN                     | vertica_kdl_dsn
SQL_MULTIPLE_ACTIVE_TXN                  | True
SQL_STRING_FUNCTIONS                     | 9732063
SQL_CONCAT_NULL_BEHAVIOR                 | 0
SQL_MAX_CATALOG_NAME_LEN                 | 0
SQL_MAX_SCHEMA_NAME_LEN                  | 128
SQL_MAX_CONCURRENT_ACTIVITIES            | 0
SQL_MAX_CURSOR_NAME_LEN                  | 0
SQL_IDENTIFIER_CASE                      | 4
SQL_CURSOR_ROLLBACK_BEHAVIOR             | 2
SQL_DBMS_VER                             | 07.00.0000
SQL_DROP_VIEW                            | 1
SQL_CHAR                                 | 0
SQL_SEARCH_PATTERN_ESCAPE                | \
SQL_REAL                                 | 07.00.0000
SQL_GROUP_BY                             | 2
SQL_DATABASE_NAME                        | 
SQL_SQL92_GRANT                          | 3440
SQL_DROP_TABLE                           | 7
SQL_ACCESSIBLE_PROCEDURES                | False
SQL_BATCH_SUPPORT                        | 3
SQL_MAX_TABLES_IN_SELECT                 | 0
SQL_ODBC_VER                             | 03.52
SQL_COLLATION_SEQ                        | 
SQL_MAX_STATEMENT_LEN                    | 0
SQL_DRIVER_VER                           | 07.00.0000
SQL_DBMS_NAME                            | Vertica Database
SQL_PARAM_INPUT_OUTPUT                   | vertica_kdl_dsn
SQL_INTERVAL_HOUR_TO_SECOND              | 0
SQL_PARAM_TYPE_UNKNOWN                   | 0
SQL_PC_UNKNOWN                           | 0
SQL_DM_VER                               | 03.52.0002.0002
SQL_CONVERT_VARCHAR                      | 12317183
SQL_DRIVER_ODBC_VER                      | 03.52
SQL_PC_NOT_PSEUDO                        | 0
SQL_INTERVAL_YEAR_TO_MONTH               | 128
SQL_PC_PSEUDO                            | vertica_kdl_dsn
SQL_INTERVAL_DAY                         | False
SQL_FORWARD_ONLY_CURSOR_ATTRIBUTES2      | 4097
SQL_FORWARD_ONLY_CURSOR_ATTRIBUTES1      | 1
SQL_KEYSET_CURSOR_ATTRIBUTES2            | 4097
SQL_SQL92_STRING_FUNCTIONS               | 255
SQL_CATALOG_TERM                         | 
SQL_INDEX_KEYWORDS                       | 0
SQL_CREATE_COLLATION                     | 0
SQL_AGGREGATE_FUNCTIONS                  | 127
SQL_FLOAT                                | verticaodbcw.so
SQL_IDENTIFIER_QUOTE_CHAR                | "
SQL_MAX_TABLE_NAME_LEN                   | 128
SQL_MAX_USER_NAME_LEN                    | 128
SQL_SYSTEM_FUNCTIONS                     | 7
SQL_MAX_DRIVER_CONNECTIONS               | 0
SQL_SQL92_PREDICATES                     | 16007
SQL_ODBC_INTERFACE_CONFORMANCE           | 1
SQL_SQL92_FOREIGN_KEY_UPDATE_RULE        | 0
SQL_MAX_ASYNC_CONCURRENT_STATEMENTS      | 0
SQL_NUMERIC_FUNCTIONS                    | 16121855
SQL_INSERT_STATEMENT                     | 7
SQL_KEYSET_CURSOR_ATTRIBUTES1            | 4687
SQL_CREATE_SCHEMA                        | 3
SQL_SQL92_DATETIME_FUNCTIONS             | 7
SQL_DROP_SCHEMA                          | 7
SQL_FILE_USAGE                           | 0
SQL_MAX_COLUMN_NAME_LEN                  | 128
SQL_KEYWORDS                             | 
SQL_PROCEDURES                           | False
SQL_CREATE_CHARACTER_SET                 | 0
SQL_DROP_DOMAIN                          | 0
SQL_NULL_COLLATION                       | 1
SQL_STANDARD_CLI_CONFORMANCE             | 2
SQL_TXN_CAPABLE                          | 3
SQL_SQL92_VALUE_EXPRESSIONS              | 15
SQL_MAX_COLUMNS_IN_SELECT                | 0
pooling                                  | 0
SQL_MAX_CHAR_LITERAL_LEN                 | 0
SQL_ALTER_DOMAIN                         | 0
SQL_DROP_COLLATION                       | 0
SQL_PARAM_ARRAY_SELECTS                  | 3
SQL_CURSOR_COMMIT_BEHAVIOR               | 2
SQL_SQL92_RELATIONAL_JOIN_OPERATORS      | 474
SQL_MAX_ROW_SIZE_INCLUDES_LONG           | False
SQL_MAX_COLUMNS_IN_ORDER_BY              | 0
SQL_INTERVAL_HOUR                        | 32000000
SQL_MAX_PROCEDURE_NAME_LEN               | 128
SQL_MAX_COLUMNS_IN_INDEX                 | 0
SQL_CONVERT_FUNCTIONS                    | 3
SQL_CATALOG_NAME_SEPARATOR               | .
SQL_ACCESSIBLE_TABLES                    | False
SQL_INTERVAL_DAY_TO_HOUR                 | 0
threadsafety                             | 0
SQL_SPECIAL_CHARACTERS                   | 
SQL_CREATE_VIEW                          | 1
SQL_INTERVAL_DAY_TO_SECOND               | 511
SQL_DROP_CHARACTER_SET                   | 0
SQL_USER_NAME                            | test
SQL_TIMEDATE_ADD_INTERVALS               | 511
SQL_NO_NULLS                             | 0
SQL_DATETIME_LITERALS                    | 65535
SQL_DATA_SOURCE_NAME                     | vertica_kdl_dsn
SQL_DROP_ASSERTION                       | 0
SQL_MULT_RESULT_SETS                     | True
SQL_ASYNC_MODE                           | 0
>>> 

</code>

Original comment by matthewc...@gmail.com on 21 Jan 2014 at 1:21

chornbeak / pyodbc

python3 + rpy + pyodb + vertica 7 = Linux segfault #354